diff --git a/cacholote/clean.py b/cacholote/clean.py
index 173b49e..5ce704c 100644
--- a/cacholote/clean.py
+++ b/cacholote/clean.py
@@ -256,19 +256,21 @@ def delete_cache_files(
             return
 
         entries_to_delete = []
+        files_to_delete: set[str] = set()
         self.logger.info("getting cache entries to delete")
         with config.get().instantiated_sessionmaker() as session:
             for cache_entry in session.scalars(
                 sa.select(database.CacheEntry).filter(*filters).order_by(*sorters)
             ):
                 files = _get_files_from_cache_entry(cache_entry, key="file:size")
-                if any(file.startswith(self.urldir) for file in files):
+                if (
+                    not self.stop_cleaning(maxsize)
+                    and any(file.startswith(self.urldir) for file in files)
+                ) or (set(files) & files_to_delete):
                     entries_to_delete.append(cache_entry)
                     for file in files:
                         self.pop_file_size(file)
-
-                if self.stop_cleaning(maxsize):
-                    break
+                        files_to_delete.add(file)
 
             if entries_to_delete:
                 self.logger.info(
diff --git a/cacholote/extra_encoders.py b/cacholote/extra_encoders.py
index 2509951..603a0f1 100644
--- a/cacholote/extra_encoders.py
+++ b/cacholote/extra_encoders.py
@@ -129,6 +129,10 @@ def _logging_timer(event: str, **kwargs: Any) -> Generator[float, None, None]:
         context.upload_log(f"end {event}. {_kwargs_to_str(**kwargs)}")
 
 
+class InPlaceFile(io.FileIO):
+    pass
+
+
 class FileInfoModel(pydantic.BaseModel):
     type: str
     href: str
@@ -389,27 +393,35 @@ def _store_io_object(
 
 def dictify_io_object(obj: _UNION_IO_TYPES) -> dict[str, Any]:
     """Encode a file object to JSON deserialized data (``dict``)."""
+    is_in_place = isinstance(obj, InPlaceFile)
     settings = config.get()
 
     cache_files_urlpath = settings.cache_files_urlpath
-    fs_out, *_ = fsspec.get_fs_token_paths(
-        cache_files_urlpath,
-        storage_options=settings.cache_files_storage_options,
-    )
 
     if urlpath_in := getattr(obj, "path", getattr(obj, "name", "")):
         fs_in = getattr(obj, "fs", fsspec.filesystem("file"))
-        root = f"{fs_in.checksum(urlpath_in):x}"
-        ext = pathlib.Path(urlpath_in).suffix
-        urlpath_out = posixpath.join(cache_files_urlpath, f"{root}{ext}")
+        if is_in_place:
+            urlpath_out = urlpath_in
+        else:
+            root = f"{fs_in.checksum(urlpath_in):x}"
+            ext = pathlib.Path(urlpath_in).suffix
+            urlpath_out = posixpath.join(cache_files_urlpath, f"{root}{ext}")
     else:
         root = hashlib.md5(f"{hash(obj)}".encode()).hexdigest()  # fsspec uses md5
         urlpath_out = posixpath.join(cache_files_urlpath, root)
 
+    if is_in_place:
+        fs_out = fs_in
+    else:
+        fs_out, *_ = fsspec.get_fs_token_paths(
+            cache_files_urlpath,
+            storage_options=settings.cache_files_storage_options,
+        )
+
     with utils.FileLock(
         fs_out, urlpath_out, timeout=settings.lock_timeout
     ) as file_exists:
-        if not file_exists:
+        if not (file_exists or is_in_place):
             if urlpath_in:
                 _store_file_object(fs_in, urlpath_in, fs_out, urlpath_out)
             else:
diff --git a/tests/test_50_io_encoder.py b/tests/test_50_io_encoder.py
index d1af15f..b3c40ea 100644
--- a/tests/test_50_io_encoder.py
+++ b/tests/test_50_io_encoder.py
@@ -9,6 +9,7 @@
 from typing import Any
 
 import fsspec
+import fsspec.implementations.local
 import pytest
 import pytest_httpserver
 import pytest_structlog
@@ -235,3 +236,16 @@ def test_io_logging(
         },
     ]
     assert log.events == expected
+
+
+def test_io_in_place_file(tmp_path: pathlib.Path) -> None:
+    @cache.cacheable
+    def cached_in_place_open(path: str) -> io.FileIO:
+        return extra_encoders.InPlaceFile(path, "rb")
+
+    tmpfile = tmp_path / "test.txt"
+    fsspec.filesystem("file").touch(tmpfile)
+
+    output = cached_in_place_open(str(tmpfile))
+    assert isinstance(output, fsspec.implementations.local.LocalFileOpener)
+    assert output.name == str(tmpfile)
diff --git a/tests/test_60_clean.py b/tests/test_60_clean.py
index 688b7b8..3efe013 100644
--- a/tests/test_60_clean.py
+++ b/tests/test_60_clean.py
@@ -5,7 +5,7 @@
 import os
 import pathlib
 import time
-from typing import Any, Literal
+from typing import Any, BinaryIO, Literal
 
 import fsspec
 import pydantic
@@ -411,3 +411,31 @@ def test_clean_multiple_urlpaths(tmp_path: pathlib.Path, use_database: bool) ->
         clean.clean_cache_files(maxsize=0, use_database=use_database, depth=2)
     assert not cached_file1.exists()
     assert cached_file2.exists()
+
+
+def test_clean_duplicates(tmp_path: pathlib.Path) -> None:
+    con = config.get().engine.raw_connection()
+    cur = con.cursor()
+
+    # Create file
+    tmpfile = tmp_path / "file.txt"
+    fsspec.filesystem("file").pipe_file(tmpfile, ONE_BYTE)
+
+    @cache.cacheable
+    def func1(path: pathlib.Path) -> BinaryIO:
+        return path.open("rb")
+
+    @cache.cacheable
+    def func2(path: pathlib.Path) -> BinaryIO:
+        return path.open("rb")
+
+    fp1 = func1(tmpfile)
+    fp2 = func2(tmpfile)
+    assert fp1.name == fp2.name
+
+    cur.execute("SELECT COUNT(*) FROM cache_entries", ())
+    assert cur.fetchone() == (2,)
+
+    clean.clean_cache_files(maxsize=0)
+    cur.execute("SELECT COUNT(*) FROM cache_entries", ())
+    assert cur.fetchone() == (0,)